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From 1996 19 species from 9 fish families have been recorded in the water bodies of Nature reserve Škocjanski zatok. Among them, at least 9 are considered as truly freshwater species.
The lis of the recorded fish species:

  1. Western Mosquitofish (Gambusia affinis)
  2. Mediterranean Killifish (Aphanius fasciatus)
  3. Golden Grey Mullet (Liza aurata)
  4. Thin-lipped Grey Mullet (Liza ramada)
  5. Leaping Grey Mullet (Liza saliens)
  6. Striped Mullet also known as Flathead Grey (Mugil cephalus)
  7. Thick-lipped Grey Mullet (Chelon labrosus)
  8. Three-spined Stickleback (Gasterosteus aculeatus aculeatus)
  9. Crucian Carp (Carassius carassius)
  10. Prussian Carp (Carassius gibelio)
  11. Roach (Rutilus rutilus)
  12. European Chub (Leuciscus cephalus)
  13. Rudd (Scardinius erythrophthalmus)
  14. Grass Goby (Zosterisessor ophiocephalus)
  15. Caucasian Dwarf Goby (Knipowitschia caucasica)
  16. European eel (Anguilla anguilla)
  17. Brown Bullhead (Ameiurus nebulosus)
  18. Big-scale Sand Smelt (Atherina boyeri)
  19. Atherina spp.

Invasive species are Western Mosquitofish and two freshwater species – Brown Bullhead and Prussian Carp – which were introduced to the Rižana River.

In 2011 a new research of fish in the lagoon of Škocjanski zatok was carried out aiming to provide an ichtiofaunistic overview of the lagoon a few years after its restoration. The results will soon be posted on the website.